Quantum chemical characterization of the cytosine: 2-aminopurine base pair

The nature of the base pairing between cytosine and 2-aminopurine is investigated by means of quantum mechanical calculations including electron correlation and accounting for the effects of aqueous solvation. At neutral pH, both a neutral wobble base pair and a Watson-Crick-like base pair having a protonated 2-aminopurine are predicted to be close to one another in energy; other previously proposed forms are found to be too high in energy to be of significant chemical interest. Accounting for the energetics of helix embedding suggests that the equilibrium between the two low-energy motifs is quite sensitive to local environment.